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Figure 6 | BMC Bioinformatics

Figure 6

From: Using structural motif descriptors for sequence-based binding site prediction

Figure 6

Work flow. a) All instances for interactions between family A and family B with identical geometric interface classification are retrieved from SCOPPI. Interface residues are indicated in the accompanying multiple sequence alignments. b) Interface columns are defined by columns with more than 50% interface residues. Interface segments are defined by including interface flanking columns. c) HMMs are constructed for each interface segment using HMMer's hmmbuild. d) HMMs are merged by insert states with high self-loop probabilities as to model the non-interacting linker region e) The collection of all merged HMMs constitutes the descriptor library. f) Sequence searches against Swiss-Prot and uncharacterized sequences with all descriptors were done using HMMer's hmmsearch

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